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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOMAL DECODING SITE IN COMPLEX WITH SISOMICIN (C2 FORM)
 
Authors :  J. Kondo, M. Koganei, T. Kasahara
Date :  18 May 12  (Deposition) - 15 Aug 12  (Release) - 05 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Decoding, Ribosome, Rna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kondo, M. Koganei, T. Kasahara
Crystal Structure And Specifi C Binding Mode Of Sisomicin To The Bacterial Ribosomal Decoding Site
Acs Med. Chem. Lett. 2012
PubMed: search  |  Reference-DOI: 10.1021/ML300145Y

(-) Compounds

Molecule 1 - RNA (5'- R(P*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C) -3')
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - RNA (5'- R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)- 3')
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SIS2Ligand/Ion(1S,2S,3R,4S,6R)-4,6-DIAMINO-3-{[(2S,3R)-3-AMINO-6-(AMINOMETHYL)-3,4-DIHYDRO-2H-PYRAN-2-YL]OXY}-2-HYDROXYCYCLOHEXYL 3-DEOXY-4-C-METHYL-3-(METHYLAMINO)-BETA-L-ARABINOPYRANOSIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREC A:4 , G A:5 , U A:6 , C A:7 , A A:8 , C A:9 , HOH A:203 , HOH A:209 , G B:39 , A B:41 , G B:42 , U B:43 , HOH B:201 , HOH B:203 , HOH B:208BINDING SITE FOR RESIDUE SIS A 101
2AC2SOFTWAREG A:16 , A A:18 , G A:19 , U A:20 , C B:27 , G B:28 , U B:29 , C B:30 , A B:31 , C B:32 , C B:46 , HOH B:210 , HOH B:211 , HOH B:218BINDING SITE FOR RESIDUE SIS B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F8U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F8U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F8U)

(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:RNA  Length:22
                                                     
                  4f8u A  2 UGCGUCACACCGGUGAAGUCGC 23
                                    11        21  


Chain B from PDB  Type:RNA  Length:21
                                                    
                  4f8u B 26 GCGUCACACCGGUGAAGUCGC 46
                                    35        45
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4F8U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F8U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F8U)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

4f8v